User: jevanveen

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jevanveen20
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Posts by jevanveen

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Comment: C: Bonferroni multiple corrections question
... This is fantastically helpful and straight to the point. Thank you very much!!! ...
written 7 days ago by jevanveen20
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Bonferroni multiple corrections question
... Hello Biostars! I have been analyzing some single cell RNA sequencing data, which compares neural transcriptomes from mice treated with either vehicle, or a drug. All the basic stuff is going fine. When I get my clusters, I find not many *super* interesting significant drug induced DEGs. If I do ...
scrna-seq rna-seq gsea statistics written 8 days ago by jevanveen20 • updated 7 days ago by dsull210
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Comment: C: Single cell RNA-seq guided correlation analysis
... Hey I know much time has passed, but I went with your suggestion #1, it looked great, and now it is part of my published work: https://elifesciences.org/articles/43668 so thank you very much again! Ed ...
written 8 days ago by jevanveen20
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QC before single cell RNA seq?
... Background: We have done single cell RNA seq, it went well, and we are preparing to do more projects. When we did it the first time, we troubleshot our cell dissociation protocol and made sure that we could get good RINs from bulk RNA before proceeding. Now we are dealing with projects that have f ...
qc rna-seq single cell written 16 months ago by jevanveen20
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Comment: C: Single cell RNA-seq guided correlation analysis
... Thank you - very helpful insights ...
written 17 months ago by jevanveen20
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Comment: C: Single cell RNA-seq guided correlation analysis
... Thank you - I was playing with WGCNA a bit before posting this, but it seems to do whole transcriptome clustering, whereas I want to specifically start with an a priori list that I took from an scRNA seq paper to asses coordinate regulation of cell differentiation state. It kind of sounds like this ...
written 17 months ago by jevanveen20
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Answer: A: How to analyse RNA-Seq data with JUST geneID and TPM values
... DESeq2 is probably what you want. It does a fine job of giving you DE genes starting with TPM values generated by Kallisto or Salmon. There's a user friendly interface available (free) at usegalazy.org ...
written 17 months ago by jevanveen20
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Single cell RNA-seq guided correlation analysis
... I would very much appreciate help with what is probably a pretty basic question. First, the question stated as succinctly as I can: ** Using an a priori list of genes, what is the best way to: 1. Test if their expressions correlate with one another across different RNA- SEQ samples? 2. Rank all ...
basics correlation rna-seq written 17 months ago by jevanveen20 • updated 17 months ago by munizmom60
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How to add tdtomato to mouse genome for RNA seq analysis
... Hello all! I am currently analyzing some RNA seq data derived from mice that express the reporter, tdtomato, under an endogenous promoter. I'd like to get read counts for tdtomato, but obviously it isn't part of the mouse transcriptome, and therefore Salmon doesn't map reads to it. From what I ca ...
salmon rna-seq written 18 months ago by jevanveen20 • updated 12 days ago by findingdan0

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Popular Question 13 months ago, created a question with more than 1,000 views. For Single cell RNA-seq guided correlation analysis

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